• The Process Folder has a macro-like utility that can do commands from this list , as well as buttons for various operations on a folder full of files.
  • Color images are read in as gray level (RGB TIFF, GIF and JPEG, whether or not the 'File / Open color files as    graylevel' command has been set to 'yes'.
  • Also note that although Lispix assumes that a file without an extension is a TIFF image file when using 'file / open', the process
    folder tool will ignore it.  Files that this tool sees have the extensions listed in 'TOOLS / file utilities / Help / file-types'.  Add the .tif extension to selected files in a folder using

    'Process folder / change file names / change extensions'.
• pfldr text file         This file lists the processing steps for the 'Process folder' command.  Make it, then assign it.
  • Make             
    • Make boiler plate for the pfldr text file.  Select default read, write, and perhaps blob directories first.
    • Note that a text file can be made in any text editor.  It needs only the lines with commands - it ignores text in a line beginning with semicolons.
  • Save & Assign           
    • Saves the window you just edited in the write folder (where the images will go), and assignes it in the Process Folder Tool for use
    • The file is automatically named process-images.txt.  If a file of that name is already there, the new file name will be process-images-2.txt, and so on.  This is to prevent overwriting the file.
  • Assign existing file
    • To use a file previously made by "Make" above, rather than making a new one.  Usually for contiuing an interrupted job.
• Process Folder!
  •   Process all of the files in the default image read folder, writes the processes files into the default image write folder.
  •   Can be stopped and continued later.

Note about blobbing.

The blob command will blob an image, generating object or particle outlines, rather than another image.   A blob file ".sblob" is the result of this processing, rather than a tiff

image, the sblob files are written to the blob directory, and a dummy tif file is written to the write directory.  This is because there can be several sblob files for the same image, with different parameters - and this is difficult to check at the top level of processing a folder.  The dummy files keep track of what images have been processed, so that the process folder command can be continued if interrupeted part way through. Interrupt processing the folder by closing the window with the progress bar and time estimates (the loop monitor window).

• Image Info
  •       Size & Limits    
    • Size and limits for folder of images
    • Fast because it does not display the images.
  •       List bad file names    
  • Lists file names with non alpha numeric characters that are not accepted on some other computer systems.                        
• Mosaic                 
  •       of folder       
    •   Makes one image that is a thumbnail sheet or 'contact print' sheet of the selected images.  Clipped scaling.  Images shrunk as needed.
• Change file names      
  • Utilities for removing version numbers, doing a global search and replace for all the file names, etc.  Make sure none of the files is in use by another program, or Lispix might error out.
• Scale Bars       
  • Lists locations of scale bars in images.
  • For determining micrograph magnifications semi-automatically from the scale bar annotations in them.  Lispix finds and measures the scale bars.  You read and type in the size and units.
•       List locations to file       
  • Locations file and fail file in aux-directory.
  • Locations file is text, tab delimited.  Collumns are: image name, x1 y1 x2 y2.     
•       Save Fragments   
  • For faster reading of sizes and units.
  •   Saves portion of image including scale bar (to check for proper location) and size annotations.This image fragment displays much faster. Fragments saved in aux2-directory.
•       List readings to file        
  • View fragments, type length and units, which are listed to the readings file in the aux1-directory.  The readings file has the same form as the locations file, with the size and units in two additional collumns.
  • * Orig images:    default image read directory.  Used to get a list of the images, but images are not loadedif the image fragment is there.
  • * Locations file:       aux directory.
  • * Fragment directory:   aux2  directory.
  • * Readings file:        aux directory.
• Progress bars    
  •       Make images      
  • Makes small images with progress bars for pasting into frames of a movie.
  • Uses a spreadsheet (chart) to give the length of the bar for each frame by name.
  • For making scales for movies.  Reads progress bar values from a spreadsheet.
  • The spreadsheet needs a collumn labbeled "image" and another labeled "progress bar".
  • The "image" collumn should have the image names (do not need extension).
  • The values for the progress bar should range from 0 to 1.0.
  • The blank image for the progress bar is the front image.  It is repeatedly copied, the progress bar filled in, and saved with the appropriate name as a TIFF file to the write directory.
  • The fill value for the bar is 255.